26,884 Works

Insights into the Mechanism of Asparagine-Linked Glycosylation: Kinetic Studies with Substrates and Inhibitors

Tamara Lynn Hendrickson
Investigations into the mechanism of action of oligosaccharyl transferase (OT), the enzyme that catalyzes the first committed step in the biosynthesis of all asparagine-linked glycoproteins, were conducted. Research focused on kinetic studies with small reactive molecules and tripeptide substrates and inhibitors; these experiments were designed to specifically probe the OT active site. Commercially available chemical modification agents were used to identify a reactive cysteine residue in or near the oligosaccharide binding site. Based on this...

Identification of New OPA1 Cleavage Site Reveals that Short Isoforms Regulate Mitochondrial Fusion

Ruohan Wang
OPA1 is a 120kDa large GTPase belonging to the dynamin superfamily. It is the only known mitochondrial inner membrane fusion protein, mediating fusion of the mitochondrial inner membranes following outer membrane fusion. Additionally, OPA1 also regulates cristae morphology and maintains respiratory chain function. OPA1 has two forms—inner-membrane-anchored long forms (l-OPA1) and cleaved inter-membrane-space only short forms (s-OPA1). L-OPA1 are proteolytically processed by two mitochondrial proteases—OMA1 and YME1L, acting at cleavage sites S1 and S2 respectively,...

Microfluidic EPG Recordings Show Striking Pharyngeal Pumping Phenotype in a C. elegans Alzheimer's Disease Model

Janis C Weeks, Kristen J Robinson, Benedicta Wanjeri, Philip F Copenhaver & William M Roberts
Strain CL4176 accumulates human amyloid-β1-42 in body wall muscles after animals are shifted from 15 to 25 oC, causing paralysis (Link et al. 2003). We temperature-shifted worms at early L4 and quantified pharyngeal pumping at 48 h using a microfluidic electropharyngeogram (EPG) recording platform (Lockery et al. 2012; Weeks et al. 2016). Recordings were made in M9 buffer with 10 mM serotonin and analyzed by automated pump-recognition software. At 48 h, control CL802 worms showed...

Mutations in KCNQ potassium channels cause pharyngeal pumping defects in C. elegans

Yoanne Clovis, Alexis Webb, Carl Turner & Bill Roberts
Pumps were stimulated with 10mM 5HT in M9 recorded as electropharyngeograms (EPGs) for 2 minutes in a NemaMetrix ScreenChip, and analyzed using NemAnalysis software (NemaMetrix). The null mutant strains kqt-1(aw3) and kqt-3 (aw1) were kindly donated by Dr. Aguan Wei (Wei et al., 2002) A) Pump frequency in kqt-1(aw3) animals was significantly lower than in N2s, while kqt-3(aw1) worms showed an increase in pump frequency (*p<0.05; ***p<0.01; 1-tailed Mann-Whitney U-test; n = 21-23 worms in...

Gene bashing of ceh-6 locus identifies genomic regions important for ceh-6 rectal cell expression and rescue of its mutant lethality

Arnaud Ahier, Shashi Kumar Suman & Sophie Jarriault
Loss of the activity of certain genes, such as ceh-6, can lead to lethality at early developmental stages, precluding the study of their function later on during development. Indeed, it was reported that more than 80% of ceh-6(mg60) animals died during embryogenesis exhibiting various phenotypes, including an abnormal rectal area and absent excretory canal cell (Bürglin and Ruvkun 2001). mg60 is a 1.4kb deletion allele that removes ceh-6 second exon and is believed to cause...

Variation between nematodes in a multi-sensory behavioral assay

Renae Ellis & Gareth Harris
An environment is often represented by numerous sensory cues. In order to better survive, an animal often needs to detect and process sensory cues simultaneously to make an appropriate behavioral decision. The Caenorhabditis elegans (C. elegans) genome encodes homologues of a significant number of molecules expressed in mammalian brains, which allows characterizing of the molecular and circuit basis for multi-sensory behavior during decision-making (Bargmann, 1998). In addition, studies have demonstrated various genes and neurons in...

Expression of an endosome-excluded Cd63 prevents axis elongation in Xenopus

Jennifer Kreis, Ramona Bonß, Kerstin Feistel & Philipp Vick
Cd63 is an adapter protein belonging to the tetraspanin family. As other members, it possesses four membrane-spanning domains, two extracellular loops, and the N- and C-terminus both face the cytoplasm. Cd63 is highly enriched in intraluminal vesicles (ILV) of late endosomes (LE; also called multivesicular bodies, MVB; Termini and Gillette, 2017). Cd63 trafficking to LE occurs via classical routes, i.e. from the ER to the Golgi complex, then to the plasma membrane, from where it...

The tetraspanin Cd63 is required for eye morphogenesis in Xenopus

Jennifer Kreis, Ramona Bonß & Philipp Vick
Tetraspanins (TSPAN) are a family of (33 in humans) scaffold proteins consisting of the name-giving four membrane-spanning domains, two extracellular loops, and an intracellular N- and C-terminus. By forming ‘tetraspanin-enriched microdomains’ they participate in organizing the plasma membrane and serve as multipurpose adapters. Some can be found ubiquitously in most cells, while others are specific to certain cell types. On a subcellular level, enrichment in distinct membrane-associated organelles has been documented for several members (Termini...

Evidence of slightly increased Pol II pausing in UPF1-depleted Drosophila melanogaster cells

Anand K Singh, Jie Zhang, Daniel Hebenstreit & Saverio Brogna
UPF1 is an RNA helicase that scans RNA to unwind secondary structures and to displace associated factors (Franks et al., 2010; Fiorini et al., 2015; Lee et al., 2015; Kanaan et al., 2018). UPF1 has been mostly studied for its role in nonsense mediated mRNA decay (NMD) and other translation-dependent RNA quality-control pathways in the cytoplasm (Isken and Maquat, 2008; Kim and Maquat, 2019). However, we have recently reported that UPF1 associates, genome wide, with...

Kepler KOI Positional Probabilities

Kepler Mission product that contains information on the possibility of the transit signal arising from an astrophysical source other than the target star. This dataset or service is made available by the NASA Exoplanet Science Institute at IPAC, which is operated by the California Institute of Technology under contract with the National Aeronautics and Space Administration.

Single-cell resolution long-term luciferase imaging in cultivated Drosophila brains

Frank K. Schubert, Charlotte Helfrich-Förster & Dirk Rieger
In Drosophila melanogaster, approximately 150 so-called clock neurons express the molecular components of the circadian clock mechanism. The activity of these neurons enables the fly to anticipate and track cyclic changes in their environment and to respond to them accordingly. The core of the circadian clock is built by two interlocked transcriptional feedback loops. In the first loop, the transcription factors CLOCK (CLK) and CYCLE (CYC) initiate the expression of the core clock proteins PERIOD...

The salt-inducible kinase KIN-29 regulates lifespan via the class II histone-deacetylase HDA-4

Tatiana Nikooei, Aja McDonagh & Alexander M. van der Linden
kin-29 encodes the C. elegans homolog of mammalian Salt-Inducible Kinases (SIKs). kin-29 mutants are small, have increased propensity to develop into non-reproductive dauer larvae, have reduced chemoreceptor gene expression (Lanjuin and Sengupta, 2002; van der Linden et al.., 2007), have reduced cellular ATP despite increased fat stores, and show reduced sleep (Grubbs et al., 2020). KIN-29 phosphorylates and inhibits the class II histone deacetylase 4 homolog HDA-4 to regulate gene expression in sensory neurons (van...

Spontaneous neoplasia in the western clawed frog Xenopus tropicalis

Makoto Suzuki, Takeshi Igawa, Nanoka Suzuki, Hajime Ogino & Haruki Ochi
Xenopus tropicalis is an excellent model organism for studies on vertebrate development and regeneration (Horb et al., 2019) and is also useful for the study of tumor formation (Van Nieuwenhuysen et al., 2015; Naert et al., 2016). Spontaneously occurring neoplasia in amphibians have been reported, such as in X. laevis, Rana pipiens, and Andria japonicus (McKinnell et al., 1968; Meyer-Rochow et al., 1991; Kawasumi et al., 2012). In X. laevis, one of 4,000 frogs (a...

Loss of nucleosome remodelers CHRAC/ACF does not sensitize early Drosophila embryos to X-rays

Alessandro Scacchetti & Peter B. Becker
The ‘Chromatin Accessibility Complex’ (CHRAC) and ‘ATP-utilizing chromatin assembly and remodeling factor’ (ACF) of Drosophila melanogaster are chromatin remodeling complexes that slide nucleosomes (Becker and Horz, 2002). Both originate from the association of the ATPase ISWI and a large subunit ACF1. CHRAC contains two additional histone-fold subunits, CHRAC-14 and CHRAC-16 (Corona et al., 2000), but its nucleosome sliding activity is essentially similar to ACF in vitro (Hartlepp et al., 2005). CHRAC/ACF are implicated in several...

Kepler Certified False Positives

This Kepler Mission product contains information about the False Positive nature of Kepler Objects of Interest as determined by the Kepler False Positive Working Group. This dataset or service is made available by the NASA Exoplanet Science Institute at IPAC, which is operated by the California Institute of Technology under contract with the National Aeronautics and Space Administration.

Kepler MIssion Completeness and Reliability Products

This dataset contains data products produced by the Kepler Project related to completeness and reliability of the Kepler pipeline. This dataset or service is made available by the NASA Exoplanet Science Institute at IPAC, which is operated by the California Institute of Technology under contract with the National Aeronautics and Space Administration.

The C. elegans TRPV channel proteins OSM-9 and OCR-2 contribute to aversive chemical sensitivity

Emily A. Mehle, Savannah E. Sojka, Medha K.C., Rosy M. Zel, Sebastian J. Reese & Denise M. Ferkey
Transient receptor potential (TRP) channels are a family of cation channels that are important for response to diverse external stimuli across eukaryotes (Venkatachalam and Montell 2007; Samanta et al. 2018). In C. elegans, only members of the TRPV family, which includes osm-9, ocr-1, ocr-2, ocr-3 and ocr-4 (Colbert and Bargmann 1995; Colbert et al. 1997; Tobin et al. 2002), have been shown to play a role in chemosensory behavior (Bargmann 2006). OSM-9 and OCR-2 are...

High Fidelity Probe and Mitigation of Mirror Thermal Fluctuations

Tara Chalermsongsak
Thermal noise arising from mechanical loss in high reflective dielectric coatings is a significant source of noise in precision optical measurements. In particular, Advanced LIGO, a large scale interferometer aiming to observed gravitational wave, is expected to be limited by coating thermal noise in the most sensitive region around 30–300 Hz. Various theoretical calculations for predicting coating Brownian noise have been proposed. However, due to the relatively limited knowledge of the coating material properties, an...

Dynamic Rupture Simulation Integrated with Earthquake Observations

Yihe Huang
Dynamic rupture simulations are unique in their contributions to the study of earthquake physics. The current rapid development of dynamic rupture simulations poses several new questions: Do the simulations reflect the real world? Do the simulations have predictive power? Which one should we believe when the simulations disagree? This thesis illustrates how integration with observations can help address these questions and reduce the effects of non-uniqueness of both dynamic rupture simulations and kinematic inversion problems....

Seismic Structure along Transitions from Flat to Normal Subduction: Central Mexico, Southern Peru, and Southwest Japan

Sara Lyn Dougherty
The fine-scale seismic structure of the central Mexico, southern Peru, and southwest Japan subduction zones is studied using intraslab earthquakes recorded by temporary and permanent regional seismic arrays. The morphology of the transition from flat to normal subduction is explored in central Mexico and southern Peru, while in southwest Japan the spatial coincidence of a thin ultra-slow velocity layer (USL) atop the flat slab with locations of slow slip events (SSEs) is explored. This USL...

Electronic States in Disordered Topological Insulators

Kun Woo Kim
We present a theoretical study of electronic states in topological insulators with impurities. Chiral edge states in 2d topological insulators and helical surface states in 3d topological insulators show a robust transport against nonmagnetic impurities. Such a nontrivial character inspired physicists to come up with applications such as spintronic devices [1], thermoelectric materials [2], photovoltaics [3], and quantum computation [4]. Not only has it provided new opportunities from a practical point of view, but its...

The Search for Gravitational Waves from the Coalescence of Black Hole Binary Systems in Data from the LIGO and Virgo Detectors. Or: A Dark Walk through a Random Forest

Kari Alison Hodge
The LIGO and Virgo gravitational-wave observatories are complex and extremely sensitive strain detectors that can be used to search for a wide variety of gravitational waves from astrophysical and cosmological sources. In this thesis, I motivate the search for the gravitational wave signals from coalescing black hole binary systems with total mass between 25 and 100 solar masses. The mechanisms for formation of such systems are not well-understood, and we do not have many observational...

Model Predictive Control for Deferrable Loads Scheduling

Niangjun Chen
Real-time demand response is essential for handling the uncertainties of renewable generation. Traditionally, demand response has been focused on large industrial and commercial loads, however it is expected that a large number of small residential loads such as air conditioners, dish washers, and electric vehicles will also participate in the coming years. The electricity consumption of these smaller loads, which we call deferrable loads, can be shifted over time, and thus be used (in aggregate)...

Rational Design of Zinc Phosphide Heterojunction Photovoltaics

Jeffrey Paul Bosco
The prospect of terawatt-scale electricity generation using a photovoltaic (PV) device places strict requirements on the active semiconductor optoelectronic properties and elemental abundance. After reviewing the constraints placed on an "earth-abundant" solar absorber, we find zinc phosphide (α-Zn3P2) to be an ideal candidate. In addition to its near-optimal direct band gap of 1.5 eV, high visible-light absorption coefficient (>104 cm-1), and long minority-carrier diffusion length (>5 μm), Zn3P2 is composed of abundant Zn and P...

Protein Structure Refinement Algorithms

Mohsen Chitsaz
Protein structure prediction has remained a major challenge in structural biology for more than half a century. Accelerated and cost efficient sequencing technologies have allowed researchers to sequence new organisms and discover new protein sequences. Novel protein structure prediction technologies will allow researchers to study the structure of proteins and to determine their roles in the underlying biology processes and develop novel therapeutics. Difficulty of the problem stems from two folds: (a) describing the energy...

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